rs4875102

Positions:

• chr8-4427170-G-A
• chr8-4427170-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033225.6(CSMD1):​c.303-7105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 151,890 control chromosomes in the GnomAD database, including 36,526 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.69 (36526 hom., cov: 31)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

CSMD1 (HGNC:14026): (CUB and Sushi multiple domains 1) Predicted to act upstream of or within several processes, including learning or memory; mammary gland branching involved in pregnancy; and reproductive structure development. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD1	NM_033225.6	c.303-7105C>T		intron_variant		ENST00000635120.2
CSMD1	XM_011534752.3	c.303-7105C>T		intron_variant
CSMD1	XM_017013731.2	c.303-7105C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD1	ENST00000635120.2	c.303-7105C>T		intron_variant		5	NM_033225.6	P4

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104891 AN: 151772 Hom.: 36514 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.718

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.691 AC: 104946 AN: 151890 Hom.: 36526 Cov.: 31 AF XY: 0.687 AC XY: 50945 AN XY: 74196

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.718

Alfa AF: 0.633 Hom.: 3251

Bravo AF: 0.687

Asia WGS AF: 0.586 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4875102; hg19: chr8-4284692;